* Six militants killed in raid - Interior Ministry
* Insurgency spreads across biggest Arab state
* Violence expected to grow ahead of election (Adds analyst, arrests, details)
By Michael Georgy and Yasmine Saleh
CAIRO, March 19 (Reuters) - A 13-year-old boy was shot dead on Wednesday in southern Egypt in clashes between police and supporters of deposed President Mohamed Mursi of the Muslim Brotherhood, a health official said.
And in Qalubiya province, north of Cairo, two Egyptian soldiers were killed in a shootout with Islamist militants, the Interior Ministry said, adding six militants were killed and eight arrested in a raid on a weapons storage facility.
Political violence, which has dogged Egypt since a popular uprising toppled autocrat Hosni Mubarak in 2011, is expected to intensify as the country prepares for a presidential election, due in a few months, that army chief Field Marshal Abdel Fattah al-Sisi is expected to win easily.
The Interior Ministry said a brigadier general and a colonel, both bomb disposal experts, were shot dead in the raid on members of Ansar Bayt al-Maqdis, Egypt's most active militant group.
The Sinai-based group has claimed responsibility for several high-profile attacks, including an assassination attempt on the interior minister last year.
A health official later said a student, 13, was shot dead in clashes between police and pro-Mursi protesters in the city of Beni Suef, south of Cairo. The Interior Ministry said 12 protesters were arrested.
Demonstrations also erupted in the capital. Medical sources said around 40 pro-Mursi demonstrators were wounded by birdshot or tear gas near Cairo University.
AL QAEDA FLAG
Egypt has declared the Muslim Brotherhood a terrorist group, killed hundreds of its supporters and arrested thousands.
On Wednesday, about 300 women, supporters of Mursi, most of them covered from head to toe in black, protested outside Al Azhar university, a venerable centre of Islamic learning. They chanted "down with military rule."
About 500 male demonstrators later took to the streets outside Al Azhar. Police fired tear gas and birdshot at them, a Reuters witness said.
Egypt's public prosecutor ordered an investigation into a report that some Brotherhood protesters attached an al Qaeda flag on buildings at Al-Azhar.
The Brotherhood denies it has links with violent militant groups and says is committed to peaceful activism.
While the state has devastated the Brotherhood, tackling Sinai-based militant groups has proven to be a far greater challenge.
Security sources said the militants targeted on Wednesday were linked to a March 15 attack by gunmen who killed six army officers near Cairo.
The Islamist insurgency has spread from the Sinai to other parts of the Arab world's biggest nation, including Cairo, since Mursi's fall.
"The violence is likely to increase as the political process continues, especially if Field Marshal Abdel Fattah al-Sisi announces his candidacy, but it won't have a big effect on political measures," said Mohamed Gomaa, political analyst at Al-Ahram Centre for Political and Strategic Studies.
Egypt's army, the largest in the Arab world, has launched several offensives against militants in the Sinai, but Islamist fighters who have mastered the terrain remain highly effective, residents say.
In the 1990s, it took the government of former president Hosni Mubarak years to stamp out an Islamist insurgency. (Additional reporting by Mohamed Abdelalla, Omar Fahmy and Shadia Nasralla,; Editing by Janet Lawrence)